Abstract: With the sequencing of the human genome, attention in biomedical research has shifted from the analysis of individual genes to understanding the genome as a whole: how is the genome regulated and organized during cell division, differentiation, and senescence? How does this organization change with disease? The ultimate goal in studying the cell biology of the nucleus is to actually detect these dynamic genomic changes, as opposed to interpreting them from transcriptome profiling, chromatin conformation capture, or other indirect approaches. This goal is mirrored by the objective of systems biology: biological processes need to be addressed in their entirety and the resulting interpretation will yield insights that are greater than the sum of their parts. We will attempt to bridge these disciplines in our study of the relationship between form and function in the human nucleus. Our ultimate goal is to describe the overall behavior of a dynamic system, the human genome in stem cells as they differentiate, to better understand how it goes awry in disease states. Current evidence indicates that genes and chromosomes are non-randomly localized within the nucleus. For example, gene expression is related to nuclear localization, with silenced genes frequently positioned at heterochromatin and the nuclear periphery, and active genes enriched in the nuclear interior. Also, various chromosomal attributes, including gene density, size (base-pair length), and activity, contribute to their organization in mammalian nuclei. Given the growing evidence for deterministic nuclear organization, identifying how it is established and maintained has become increasingly important. We have previously demonstrated that during the differentiation of a murine stem cell to derived lineages, chromosomes form arrangements based on coordinate gene regulation. We propose that self- organization best describes how the local interactions in a gene network yield chromosome-association patterns that produce a lineage-specific topology. We aim to fully characterize the role of self- organization in genomic function during differentiation of human stem cells. We will use novel imaging techniques and analytical approaches to determine the influence of self-organization during differentiation and de-differentiation of induced pluripotent stem cells. We will utilize a transcriptional noise assay to test for underlying determinants of self-organization in the differentiation of an adult stem cell. Finally, we will test the validity of self-organization as a paradigm for nuclear dynamics by attempting to create de novo a subnuclear body of unique function by non-hierarchical assembly of nuclear proteins. Combined, these approaches will yield new insight into the effect self-organization has on the human genome during normal cellular differentiation and, through targeted perturbations, how this organization is disrupted in disease states.